When It Rains It Pours
by kwillads
Summary: John has one of those days. Rain, common cold and a mudslide add up to an intersting day. This story has three possible endings. Let me know what you think. No Beta, all mistakes are mine.
1. Chapter 1

Stargate SG-1 and Stargate: Atlantis, the characters and universe are the property of Stargate (II) Productions, Showtime/Viacom, MGM/UA, Double Secret Productions, Gekko Productions and the Sci-Fi Channel

Stargate SG-1 and Stargate: Atlantis, the characters and universe are the property of Stargate (II) Productions, Showtime/Viacom, MGM/UA, Double Secret Productions, Gekko Productions and the Sci-Fi Channel. The content of this story is solely for entertainment purposes and no copyright infringement is intended.

A/N: This story was not Betaed, all mistakes are my own. I have not seen nor read a story that had multiple endings so I thought I would give it a shot to see what FanFiction readers think. This story has three possible endings. Let me know which is your favorite if you have time.

**When It Rains It Pours**

Colonel Sheppard secluded in his quiet office was working on the security schedule for Atlantis. It was a big city and the military had a lot to secure and safeguard. He was working out where to station his men for the third time today. The schedule wasn't difficult and everytime he got close to finishing he kept getting interrupted… just like now.

"Sir…nine more men have been quarantined to their quarters." Major Evan Lorne reported standing at the threshold of the office doorway. This was the fourth time he had come to his CO's office with bad news and had been afraid to enter.

"Nine?" Questioned the Colonel looking down at his laptop in annoyance which held said schedule.

"Yes Sir."

"Major, that brings us to just over one fourth of the military populous in quarantine. How are the rest holding up?" The Colonel finally looked up from his laptop he had been studying to see that the Major was still standing in the hallway. "Lorne? Don't tell me you're coming down with this too?"

"Ah…no Sir. It's just safer out here. The last time I was here you threw a book at me; the Marine handbook no less. The rest of the men are holding up fine, so far Sir."

Washing a hand across his tired face, "yeah…sorry about that. Maybe I could order them to stay healthy."

"Yes Sir."

The Colonel noticed the broad smile that spilled across his second in command's face. "You're not helping Major."

"Sorry Sir."

It had been raining for seven solid straight days now; day and night, night and day with no signs of stopping anytime soon. The sky was overcast gray and so were the moods of the expedition member's. Those that had caught a cold were miserable and confined to quarters for the next forty-eight hours or so while they were contagious. After that, they could move about the city but most stayed in their quarters.

Off world missions were scaled back to almost non-existent due to the increase in number of military that had been quarantined. As for the medical staff they were the only ones keeping busy. Although Carson called it the 'common cold', it was the Pegasus variety. It hit fast and hard.

So far most of the expedition who contracted the cold bug had the typical cold symptoms; runny nose, nasal congestion, sneezing. There were some who got it worse. Beckett realized after the first day it had to do with the ATA gene. Those with the gene also ended up with a sore throat, cough, muscle aches, headaches and a slight fever. On average, the duration of the cold virus was eight to ten days. Even though after forty-eight hours the patient was no longer contagious they still felt like crap. For now all Carson could do was quarantine the sick, push plenty of fluids and see if the mess kitchen could make chicken soup without real chicken. A remedy his mother profusely confessed was the only cure.

The rain came down steadily pelting the stained glass windows of Atlantis. The outside temperature was moderately warm in spite of the constant rainfall. Five days ago the military took to training as much as they could to release the pent up tension of not going off world and to release the stress of pulling double shifts to cover those that had taken ill. After seven of his Marines landed in the infirmary two days after the rain had started the Colonel assigned the remaining military staff 'chores'. He assigned three teams to the jumper bay to inventory, restock and supply the jumpers. Two more teams did complete inventory of the armory. At least this gave them something to do other than having their bodies beat to a pulp by a cabin-fevered Satedan in the training gym.

Three percent of the civilian populous had been affected by the virus as well. With a quarter of his Marines down Colonel Sheppard found himself re-doing the duty assignment roster every few hours in order to cover the bare necessity of safeguarding Atlantis and its occupants.

Colonel Sheppard availed himself to be the designated 'light switch' for McKay and several of the other scientists working on Ancient tech that had been found over the past few months. Other times Sheppard kept himself busy in his office; when not playing 'light switch' he was getting his paperwork completed and filed. He caught up on requisitions; he added a few more items that his military needed to his long 'shopping' list. And every time Evan showed up at his door, he re-did the security roster as eight more Marines had caught the darn cold bug.

Before heading to bed he made his usual rounds checking on his Marines who were on patrol and some of the staff members like had been doing every night for the past four plus years. It was his job to make sure Atlantis was secure and its people safe.

It was 00:23 when Colonel Sheppard reached his quarters. It had been a long day and he was looking forward to a nice hot shower and some sleep. As the door shut behind him he sneezed, "I'm not getting sick. I'm not getting sick. I'm NOT getting sick! God I hate this rain." He groaned to himself as he sneezed once more before stripping and headed for the hot shower. The whole time he kept chanting to himself over and over, _'I'm not getting sick'_.

oOo

"_Control to Colonel Sheppard."_ Exclaimed the night duty personnel over the comm system. _"Colonel Sheppard please acknowledge!"_

"Sheppard, go ahead." The Colonel said groggily into his headset as he placed it on his ear.

"_Sir there has been a mudslide on the mainland. Halling radioed in a few minutes ago and requests assistance. He states many at the settlement are trapped."_

"Alright inform Teyla and have her meet me in the jumper bay in fifteen minutes. Sheppard out." By the time the Colonel heard 'mudslide' he had already pushed the covers aside and gotten out of bed. Adrenaline pumped through his body and had him in his uniform in no time at all. Looking at the clock on his nightstand it was 03:11. "Major Lorne." He coughed into his comm.

"_Lorne here Sir."_

The Colonel heard the sleeping Major answer. "Major we have a situation on the mainland. Mudslide and civilians trapped. Get six teams rounded up, full gear and report to the jumper bay we leave in fifteen minutes."

"_Yes Sir."_

"Doctor Beckett this is Sheppard."

"_Aye Colonel. I've just heard. I'll have my teams ready." _

"Great Doc. See ya in the jumper bay. We leave in fifteen minutes."

Colonel Sheppard actually sat down and took the time to properly lace and tie his boot laces 'tight' before grabbing his vest. Most days Sheppard just slipped his feet into his boots, tucked the laces in and called it good. Coming out of his room he met up with Teyla and Ronon on their way to the jumper bay.

As the three entered the bay it was a controlled chaos of Marines and medical personnel. The Marines were packing two jumpers with supplies under the direction of his second in command. _Damn I'm lucky to have him_ John thought. He could see lights of all types, shovels, tents, rain gear, food stuffs and bottled water all being neatly packed inside the jumpers. While the medical personnel loaded a third jumper with medical supplies, splints, oxygen tanks, backboards, blankets, gurneys and more. They never really practiced for such emergencies but from the looks of what was going on in front of him, there was no need. His military personnel were top notch.

"All right listen up." The Colonel shouted over the noise. Clearing his scratchy throat he resumed speaking as soon as the bay quieted. "We're taking six jumpers. I'll do a fly by first and decide where best to land. Once we land I want Capt. Overton and Capt. Polansky and your teams to set up two emergency tents for Dr. Beckett and his staff at the back of your jumpers. Doc I need you and your people to stay in the jumper until the tents are up. Then you can move your equipment. It won't take but a couple of minutes. Capt. Overton and his team will assist you with your gear. Captain Johnson you and your team will start unloading the food and water. I'm sure the Athosians will have a place set up. Lieutenant Manetti teams will start setting up lights and get those generators working. The rest of us will start search and rescue operations. Set your radio to channel two. If you are unsure whether or not to move a victim contact Beckett and get a medic to your location. We don't want to add to their injuries. Any questions?" The Colonel took a moment to look over the anxious faces staring back at him. "Okay let's go and be careful!"

The last of the supplies were loaded and by 03:41 and the jumpers were lifting off one by one into the dark, rain filled sky. The Colonel pushed Jumper One to its maximum limits and a little beyond in flight to reach the mainland twenty minutes later. The Colonel turned on the forward spot light as he flew over the settlement looking at the damage. The Athosian torches flickered in the heavy rain as the Athosian's worked to free their people. The Colonel decided that the field at the south end of the village would be a large enough area for the jumpers to land. He ordered Captains Overton and Polansky to land as the end of the settlement side-by-side between the last two huts.

As soon as the back hatch was down on Jumper One, Teyla ran into the dark night. Seeing Halling she ran to his side to be updated on her people. Teyla had gasped when she saw the damage from the air, but now she was finding it hard to control her thoughts and fears as she took in the sights of the settlement. Mud flooded freely through the huts like a raging river sweeping anything and everything that got in its path away. Some huts had collapsed completely while others were barely held up. Shouts and cries for help were cutting through the darkness.

Teyla instructed Captain Johnson where to take the food and water. The two tents were already put up and the medical equipment moved inside. Four generators were running and light flooded the camp and medical tents. Teyla was amazed at the speed and efficiency of what all had all been done. It had been mere moments that she talked with Halling. Teyla noticed the rest of the teams went to work digging out survivors. Teyla helped some of the injured that had been dug out already by her people into the medical tent to be cared after.

Colonel Sheppard and Ronon were working their way into their third hut. They had already taken eight people to the medical tent and three others who were uninjured to the safety of a dry hut to get warm and have some food and water. Mud was knee deep in places mid-thigh in others and it made moving almost impossible. As they breached the opening to the hut John scanned the interior with the lantern for survivors. On the far back right hand corner was a little girl of about seven or eight. She was holding onto what looked like a large doll at first, but as John and Ronon took a closer look, found that it was her younger brother. He lay limp in her arms.

The little girl was perched on a crate that was wedged into the back corner. Sheppard had seen Halling use this type of crate many times to trap with. She and her brother were covered in mud. From the looks of things, John suspected that their father got the two children up there before a section of the huts wall gave way. From the position of the father on the far left of the hut John surmised that the mud swept him to the other side of the room when the wall finally gave way. John sat the lantern down near the entrance to free up his arms and waded through the mud towards the two children, while Ronon headed for the father that was slumped up against the dining table.

"Don't be afraid my name is John. Are you hurt?" The Colonel asked as he pulled a wooden bench out of the mud and out of his path.

"I'm Tomeeka. I'm not hurt, but I think my brother is." She answered back quietly. "You're Colonel John aren't you?" She asked shyly.

"Yes sweetheart I'm Colonel John. And I'll be there in just another couple of minutes to get you and your brother to safety." His movements were slow. He was having a hard time keeping his footing. There was so much debris hidden within the mud that he kept running into things with every step. "What's your brother's name?" He asked with a sudden cough.

"His name is Pilas. Is my father all right? He was talking to me earlier, told me to stay her and hold Pilas but he has been quiet now for some time."

John looked over his shoulder to Ronon who gave a nod. "Yes Tomeeka, your father is fine he's just sleeping. Ronon is going to take him to see one of our doctors. He's going to be just fine. Where's your mother?"

"She died when my brother was born five cycles ago." She stated.

Tomeeka was keeping a firm grip on her little brother. By the time John made it to Tomeeka Ronon was back to help him. John reached over and took Pilas from his sister's grasp. Turning around he took a couple steps to meet Ronon and handed the little boy gently over. Ronon's eyes darken with sadness that the little boy was cold and limp in his arms as well. Without saying a word he bundled the small boy up under the flap of his coat and headed for the medical tent where he had taken their father.

"Okay Tomeeka let's say we get out of here." John turned back toward the little girl and when he got close enough he opened his arms and Tomeeka threw her arms around his neck and held tight while he stumbled back toward the huts opening. When the Colonel and Tomeeka reached the medical tent John sat her down on one of the open gurneys while a nurse came over to check on her. John gave the nurse what information he gleaned.

"Oh Colonel there you are. I have nine cases that need to go back to Atlantis right away. I have them all situated on the jumper. I've contacted Dr. Biro and she is expecting them." Beckett rattled off.

"Fine Doc." John replied. He was just about to tap his radio when Captain Wallace entered assisting one of the Athosians. "Captain Wallace are you available for evac?"

"Yes Sir."

"Thank you Captain. Doctor Beckett has nine patients ready for evac back to Atlantis. Doc you better send along a nurse just in case."

oOo

It had taken two more jumper flights to carry more of the wounded to Atlantis. He had been informed there were a couple of broken legs, a couple broken arms, and some cracked ribs. One case had internal bleeding. A few dislocations, some concussions and some had deep cuts that needed stitches. There were eleven dead; six adults and five children, Pilas was the youngest. Most had minor injures that were treated in the medical tent; cleaned up and bandaged.

Daylight was beginning to peer over the eastern plains. The rain had not stopped and it appeared that it was going to rain yet another day.

Colonel Sheppard rallied his troops together and offered his congratulations for a job well done. From the time the call went out for help on Atlantis to a job well executed and handled once on the mainland. The Colonel not only praised his military staff but he also praised the medical staff. He informed them that replacement personnel would arrive in a few hours. In the mean time he instructed them to continue to help and aid the Athosians the best they could. It was down to salvaging what possessions they could.

Colonel Sheppard was the epitome of a drowned rat. The scratchy throat he had hours ago now was sore and it hurt to swallow. He still coughed and sneezed and was soaked through to his skin from being out in the rain but so were the rest of his men and women who helped rescue the Athosians. He and his uniform were caked in mud from head to toe. His normally spiked hair lay limp and flat against his head.

Teyla remained with her people. Ronon requested to stay behind to help the Marines. Ronon figured he could do more good here then back on Atlantis. John headed for the jumper that was parked by the medical tent to fly back the last few injured and most of the medical staff. Carson left a doctor, nurse and had two Corpsmen's behind to help anyone that might get hurt in the salvaging operation. As the jumper rose he circled a few times taking a good look at the mudslide now that daylight had broken. He could see the destructive path of the flow and the damage it had caused to over half the settlement.

Dr. Beckett looked on as more coughs and sniffling escaped the Colonel from time to time. Although busy with the injured Beckett still kept a watchful eye on those rescuers. Making mental notes to himself of who he would need to follow up with once the crisis was over. And the fact was Lt. Col. Sheppard was at the top of his list.

"Atlantis, this is Jumper Seven inbound ETA approximately twenty-five minutes. Have Lt. Cadman meet me in the jumper bay upon my arrival. And contact Dr. Greene too. Jumper Seven out."

"_Understood. Atlantis Base out."_

Inside the jumper it was mostly quiet as he flew across the ocean away from the mainland. Jumper Seven lowered into the bay to rest on its recharging pad. The back hatch was lowered and the medical staff helped the few injured. Colonel Sheppard powered down the jumper and was last to exit. Carson had waited for him with arms crossed and a stern look.

"Colonel, I want you to report to the infirmary. I don't like the sound of that cough."

"I will Carson, I promise. But not right now." Lt. Cadman and Dr. Greene were just entering the jumper bay. "I have some things I need to take care of first. I promise Carson. You heard Elizabeth she's expecting me to report on the situation and the Daedalus is here now too so I'm sure Col. Caldwell is eagerly waiting as well." He said coughing once again holding his hand to his chest as his comm beeped in his ear. "Sheppard," listening to the other person intently. "I'm on my way Elizabeth. Sheppard out. Sorry Doc gotta go."

"Alright lad. You take care of business then come see me. I'm holdin' ya to your promise."

John nodded in agreement and turned to the Lieutenant and Dr. Greene and explained what he wanted done. Just as he finished with them Elizabeth comm'd again. As he headed out of the jumper bay and towards command he radioed McKay to get one of the eight desalination tanks full and figure a way to relocate it to the mainland. As he walked he arranged five more teams to replace those on the mainland along with additional supplies. He ordered Major Jacobs to inform the men to stay on duty and to get as many of the non-quarantined men back on duty as he could. His men were already pulling double shifts and relief would need to be coming soon. Holding his ribs tight as another coughing spell rattled his insides all he could think about was getting out of his wet uniform and into a hot shower and clean clothes. Instead he found himself in Dr. Weir's office giving an update to her and Col. Caldwell.

"Over half the settlement is gone. Eleven dead; five of those were children. Dr. Beckett brought the most injured cases here. I'm not sure of the total count, but there were broken bones, cuts and some had concussions. I'm sure he can fill you in on the details." John had to pause as a tickle in his dry throat started him to cough. "The mud was knee high or better most everywhere. Teyla and Ronon stayed behind. They have plenty of food and what fresh water we took. I've asked McKay to get one of the desalination tanks full and to figure a way to get it to the mainland he maybe asking for your help Sir. Their water source is contaminated for the time being. I've already sent five teams back to relieve personnel. I also sent our tents with the replacement teams to set up temporary housing while they rebuild. I've put Major Jacobs in charge of rounding up as many men as possible to relieve the sentry's and patrols here on Atlantis. As I flew over the area, I think I've figured a way to re-route the mud flow. I think we can create a fissure that will turn the flow away from the settlement. I have Lt. Cadman and Dr. Greene on their way now to look over the area. Dr. Greene is a Geographer and the Lieutenant can handle the ordinance I don't know how much longer this rain will keep up. In any case…" John couldn't hold back his sneeze any longer. "Pardon me. We'll need to damn up the break but won't be able to do that until this rain stops."

"Are you alright John? You look flushed." Elizabeth asked.

"Yeah…I'm good." He tried to laugh it off but ended up coughing again.

"Colonel, I understand you have a quarter of your staff down and now with the relief efforts on the mainland…but I need the Daedalus off-loaded as soon as possible." Caldwell informed knowing the Colonel would be pressed thin for staff. "We're due back ASAP to take part in an offensive strike against the Ori. I would like to get together with you and Dr. Weir at 15:00 hours for a final debriefing before the Daedalus must leave. I'd also like to review your AAR on the Athosian mudslide at that time. Would that be acceptable?" Col. Caldwell asked.

John nodded in affirmation afraid opening his mouth would have him coughing again. "That would be fine Steven fifteen hundred hours my office then." Elizabeth stated.

"I'll start on the off-loading Sir. Permission to be dismissed?"

"Permission granted."

oOo

Since Colonel Sheppard had five teams relieving the rescue team it left him short handed for the off-loading as over a quarter of the Marines were down sick. Those coming off duty had already pulled a double shift and needed to eat and sleep. Those taking their places were most likely still sick. So for the second time today he found himself outside in the rain lending a hand with as many men he could round up moving the much needed supplies across the pier from the cargo hold to the warehouse in the pouring rain. Twenty minutes into it his uniform was soaking wet, not that it had dried completely in the last forty minutes. He and his small crew managed to get the supplies off-loaded in little over three hours. He left Thompson, Meyers, Kreiger and Fallstaff in charge of disbursing with orders to get medical supplies to the infirmary first, then food stores to the mess hall, then munitions to the armory and not to worry about the science equipment or personal care packages. And finally to move the items slated for Earth to the Daedalus.

The four men divided up their tasks; Kreiger took the medical supplies to the infirmary. While Fallstaff and Thompson took munitions to the armory and left Meyers disbursing the food stores to the mess hall. In as little as two hours everything was expended even the science equipment and personal care packages. Kreiger teamed up with Meyers to help with food distributions once he had all the medical supplies delivered then the pair handled the rest. Then the four Marines gathered the crates and containers headed for Earth and took them to the loading ramp of the Daedalus.

John headed to his quarters to shower and change. As he came around the corner he bumped into Dr. Murray. She had broken her glasses in her lab and was trying to make her way back to her quarters to get her second pair. The doctor was profoundly blind without the aid of her glasses and when she got into the transporter she thought she hit the right destination location on the site panel, but ended up in the military's housing wing of Atlantis. Quite a ways from the science housing wing. John took her by the arm, apologized for the wet uniform and squishing sounds he made as he walked and together got her back to her quarters in the science wing. She was having difficulty locating her spare glasses. She couldn't remember where she kept them and with her sight problem John helped her out. An hour later the glasses were found.

Making another attempt towards his quarters to get cleaned up Mary, one of Beckett's nurses was making a supply run for the infirmary. Mary stopped the Colonel and asked for his help in carrying some supplies. He couldn't refuse knowing how many injured were in their infirmary so he patiently waited while Mary gathered up what they needed and filled his open arms. Mary had to break open several of the new shipments to get what she needed. Together, with arms full, they made their way into the busy infirmary forty minutes later.

"Thank you Colonel, for helping Mary." Carson said when he saw the two walking in with arms piled high. "I couldn't spare anyone else to go and we desperately need those supplies. Put them down right there. Now why don't you sit over there so I can have a quick look at ya." Carson pointed to an open bed while he instructed Mary on who needed what supplies.

The Colonel headed for the open bed and sat down. Maybe he could get Carson to give him something for his sore throat and cough. "Ach…what is this? You're soaking wet."

"Had to unload the Daedalus…'Sheppard'." John said into his comm effectively shutting down Carson's rant about being wet for the second time today. "Okay Sergeant I'm on my way. Sheppard out. Sorry Carson this will have to wait. We're missing two crates of P-90's and a case of ammo. I'll come back later… promise." John had already hopped down off the bed and started for the exit as he advised the doctor of the immediate situation.

oOo

"Okay Master Sergeant what have you done with my P-90's and ammo?" John inquired upon entering the armory. How could two crates of guns be missing in less than two hours? Since he was part of the off-loading team he knew everything was accounted for. His 'John Hancock' was on the bottom of each inventory sheet as each crate was coming off the Daedalus.

"Sorry Sir, haven't done anything with them since they never showed up here. All I know is we are short one hundred P-90's and a crate of ammunition to go along with it. Here are the serial numbers." Offered Chief Master Sergeant Smythers handing his CO the detailed manifest.

"Okay Chief let's double check."

For the next hour the Colonel and Smythers checked the inventory against the serial numbers and still came up two crates short. He knew it might be a waste of time since he had the armory inventoried just a few days ago, but still no rock unturned. Sheppard headed next to the warehouse where everything is stored before being disbursed to the different areas. Maybe Thompson, Meyers, Kreiger or Fallstaff missed the three creates somehow. He checked all remaining crates in the warehouse and came up empty handed for the second time in two hours. Another hour wasted. This was giving him a headache and it was getting harder to breathe with all the coughing he was doing too. Man did his chest ache. Where could they have gone? He knew they had to be here somewhere.

He pulled up his wet jacket collar around his neck a shiver ran down his spine as he pushed open the warehouse door that led onto the east pier. Rain was still pouring down as he walked the pier looking for his lost crates. The Daedalus crew had tossed out their empty broken crates and boxes not to far from the end of the Daedalus's cargo ramp. The pile took up the space of a semi's trailer, just not that high. It amazed him how much trash a three week journey through two galaxies produced. Atlantis would incinerate the empties while any good shipping crate and containers went back to Earth to be repacked. John started going through the pile of boxes as it was the last place to look on the pier.

"_McKay to Sheppard."_

"Go ahead."

"_The desalination tank is full. I've closed off and disconnected the tank. I think our best way to move it is use the Daedalus to beam it aboard into the cargo hold then down to the Athosian settlement."_

"Fine. Contact Col. Caldwell to make arrangements I've already discussed this matter with him and Dr. Weir earlier this morning. Major Lorne is still on the mainland contact him when you're ready to beam the tank down. Good work McKay."

The Colonel turned back to his present task and continued to go through the pile of broken crates. By the time he hacked and sneezed his way through most of the pile he came across his missing guns and ammo. He contacted Chief Master Sergeant Smythers and advised to get some help and come get them. He found them; he was done with this mess and wanted out of the rain. That's what being in command was all about…delegating. Right?

With that disaster adverted and the guns and ammo in the very safe and capable hands of the Chief Master Sergeant he headed once again towards his room to change out of his wet uniform. This was the third time today he'd been out in the Atlantean rain. His thoughts kept turning to a warm shower, clean clothes and now food as he headed back into the city from the east pier. He hadn't had any breakfast and it was now after lunch time. He couldn't decide whether to get food first then shower or shower then food.

Rounding the last corner that would take him to his quarters his comm link beeped in his ear. John stopped dead in his tracks right in the middle of the hallway. Head down, eyes closed. Maybe he could just ignore it. He was so close to his quarters, he could see the door from here. He could say he didn't hear it. The comm link beeped a second time…no he didn't suppose he could ignore it.

"Sheppard." He stated flatly, his voice a bit hoarse from his sore throat and all the coughing he'd done.

"Colonel I have several Athosians that can return to the mainland. And it goes without saying I could use the freed up space." Carson informed.

"Fine Doc, I'll get som…"

Carson cut the Colonel off mid-sentence. "No son, I think it best you fly them back. Most of them are children and they know you. As much as I would like to send them with someone else I think it best you do it. They're all pretty shaken up about the disaster."

"Give me thirty minutes to sho…" Shower, change and eat he wanted to say.

"The wee lads are a bit fretful. After the trauma of the flood and being away from their parents they are eager to get back Colonel."

"Fine. Round them up and I'll meet you in the jumper bay in five minutes." So much for a warm shower, clean clothes and food.

He started moving again down the hall as he came to his quarters he slowed and let slip a sigh…oh so close. He picked up his pace moved past his quarters and into the gate room, up the grand staircase, through the control room and up another flight of stairs into the flight bay. When he entered, Carson had the kids settled in the back of Jumper Three. He gave them all a friendly smile from the end of the ramp and told them they would be back with their parents in no time. The children squealed with excitement in seeing Colonel John the trauma of the morning forgotten for the time being.

"All set?" He asked Carson as he smiled at the kids in the back of the jumper.

"Aye…there ready to go. Seems you have a following Colonel. Thank you for taking them back. I'll see ya when you return."

Colonel John waded carefully through the children that were seated on the jumper floor patting heads in his attempt to reach the pilots chair. He was glad there were two adults heading back with him at least they could keep the kids seated during the flight.

Closing the ramp he did his pre-flight check. Requested clearance from flight control and soon found his way towards the mainland. Upon reaching the mainland his idea of changing the mud flow must have worked. The flow was diverted away from the settlement and towards the ocean. He circled one more time before landing. There were already two rows of tents up to provide temporary housing for the Athosians and his Marines were working on a third. With the ground sodden with rain he bet it was difficult to keep the tent stakes from collapsing.

Jumper Three settled down softly onto the muddy ground. After powering down, he made his way to the back hack release before lowering the ramp. As the ramp lowered several Marines, Teyla and Ronon along with the Athosians greeted them. They started carrying the kids off the jumper one by one and matching them up with parents or guardians.

Lt. Cadman and Dr. Greene gave a quick report on how they created the fissure and requested to stay to keep an eye on the flow. Ronon and Teyla stayed behind this trip as well. Major Lorne was overseeing the desalination tank and instructing several of the Athosians in how to get the water out. The Colonel left Jumper Three where it landed and took Jumper One back to Atlantis. By the time he would get back that left him just under an hour to write up his report for Caldwell. He passed on the thought to even try for a shower and clean clothes and headed directly to his office to start his report.

At 15:00 hours John walked into Elizabeth's office. Still in the same uniform. Still covered in mud from head to toe and completely wet again for the fourth time today. He was almost afraid to sit down since he was so dirty. Almost.

Elizabeth gasped as he entered her office. "John?"

"Hope I'm not late." He said as he sat down ignoring Elizabeth's gasp and gave them both a lopsided grin. "Here's the AAR you requested on the Athosian mudslide. I'm afraid it's not as complete as I'd hope, but I can send an updated version the next time we contact Earth. I didn't have much time to work on it." He said with a sigh handing over the computer tablet. The Colonel hit the high points so to speak in his much abbreviated report and hoped it would be satisfactory for the time being. "Thanks for the help with the water tank Sir."

Elizabeth as well as Col. Caldwell had concerned looks on their faces. Besides the uniform covered in mud, his hair laying flat for the first time, John looked exhausted and flushed. "John, how did you get so dirty just taking the children back?" Elizabeth wondered.

John was giving himself a once over before he answered. "This…this is not from the children. I haven't had time to clean up or change yet. Not to rush, but could we get this briefing started so maybe I can get cleaned up before dinner." Oh what a wondrous thought that was.

The three leaders held their briefing and by 17:50 hours had concluded. Leaving Elizabeth's office he headed to his quarters. He was stopped just outside the gate room by one of the Marine patrols and was advised that Corporal Mitchell had ended up in the infirmary due to something he ate. _At least it wasn't the cold bug_ John thought to himself. The Marine advised he had already spoken to Major Jacobs about the situation and for the Colonel to expect a call. Someone would need to fill in on Cpl. Mitchell's shift from 18:00 to 22:00 hours. As the Marine patrol moved off John's radio beeped.

John looked at his watch it was already 17:55. When he took the children to the mainland he also swapped out the teams working. Sent five refreshed teams out to replace the five that had been working since 07:30. When Mjr. Jacobs radioed he informed the Colonel there just weren't anymore available bodies. Sheppard quickly ran down the mental list of personnel who could take Corporal Mitchell's duty and came up with the same conclusion. Sheppard advised the Major he would take the duty.

By passing the mess hall he headed for the armory to check out a P-90 and grab his gear. He needed to be in Section 8 in…well looking at his watch he needed to be there three minutes ago to relieve Sergeant Moore. As he walked out onto the outside walkway he relieved Sgt. Moore and apologized for being late. He began his sentry watch moving between Section 8 and Section 13 on the outdoor walkway. The Marines taking duty inside Atlantis had been working double shifts for a week now ever since the cold bug struck down a fourth of his troops. Yet those who were rotated to duty outside maintained a four hour shift since the current weather elements were not so pleasing. Colonel Sheppard and Major Jacobs both agreed to keep those pulled off sick leave inside Atlantis. No need to add pneumonia to their already compromised immune systems.

The rain pelted him as he walked back and forth. He didn't see the need to put on rain gear since he was still a bit wet from earlier. The temperature outside was nice, not cold at all. Maybe his uniform would be clean by the time his shift was over. John always tried to look on the bright side of any situation. However today it was taxing. God he hated the rain right now.

Carson comm'd him about half way through his duty. "Colonel I'm still waiting for ya to keep your promise."

"I know Carson I know. It'll have to wait a couple more hours. I don't get relieved until 22:00 hours."

"What do ya mean 'get relieved'?" Carson inquired.

"I'm on sentry duty Carson. Corporal Mitchell got ill and is in your infirmary. There was no one else who could fill in. I already have some of the non-contagious personnel back on duty to help out." Sheppard explained trying to cover up hacking up his left lung.

"Aye the lad is here. Alright Colonel I'll see you at 22:00 hours them. Beckett out."

oOo

It was now 22:37 and still no Colonel in the infirmary. Carson picked up his doctor bag and headed for the Colonel's quarters. Not getting any response from knocking or the door chime Carson used his medical override to open the door and let himself in. The lights were off, but he thought them up just a little in case the Colonel had fallen asleep. As the lights came up enough for him to see he found the room empty and his bed looked like someone had left in a hurry. Carson made himself comfortable in the desk chair to wait. The Colonel was not getting out of his promise or this exam.

The door swished open and a very tired and wet Colonel stepped in. The lights were up enough that he made out a still figure slumped over his desk. Soft snores emanated from the motionless figure. John looked at his watch it was after midnight and he debated whether or not to wake the sleeping man or let him rest. It had been a long day for both of them. Before he could make up his mind he sneezed which led into coughing. Groaning and holding his ribs tight as he almost doubled over. Carson's head rose from the desk and blinked the figure standing at the door into focus.

"Colonel where have ya been? You said you got off duty at 22:00. I've been waitin' for ya." Carson moved to help the Colonel settle the coughing fit by getting him a glass of water. "Just sip it for now."

"Thanks." John managed to breathe out.

"You look awful lad. Let me help ya get out of those wet clothes." Carson reached for the zipper on the tac vest and was startled by just how wet the Colonel's uniform actually was. "Ach…you're soaked to the bone."

John waved and flailed his hands to get Carson to stop. He was old enough to get undressed without any help. "I can do it. Just give me a minute." The Colonel bit out angrily. He moved over to his nightstand and took off his comm and laid it down along with his watch and gun. Not realizing he turned his radio on.

"Okay just get out of those wet things. It's after midnight. Where have ya been lad?" Carson asked again turning to the Colonel's dresser to take out some dry clothes for the pilot to put on.

"Well when I got done with sentry duty I went to Elizabeth's office."

"A meetin' this late? She ought to be ashamed of herself. She should be…"

"No. No meeting. She just forgets when to call it a day." John explained while he sat down on the trunk at the end of his bed to untie and remove his soaked and dirty boots. Each sock made a wet 'plop' sound as they landed on the floor.

"Lad you're not making any sense." Handing the Colonel a dry shirt, pants and socks.

"It started a long time ago Carson. When we first got here there was a lot to do." John managed to get out before he started coughing again. "Many nights when I was on late duty I would find Elizabeth still at work in her office. Sometimes she was still there at five am." John paused while Carson checked his temperature. "After a couple of weeks of this I could see that she was run down. So I started to go to her office around 21:30 hours to kind of…bug her. Distract her enough that she could not concentrate or would get upset at me and finally call it a night. Then I would walk her to her quarters apologizing the whole way of course." The Colonel had put the clothes the doctor handed him down on the bed beside him and was in the process of getting out of his wet BDU's.

"I see. You have a temperature Colonel. Almost one hundred and two. So it took you two hours to get her to her quarters tonight?"

"No. She's used to it now. When I show up at her door, she stops working."

"That still doesn't explain where you've been." Carson added listening to John's lungs. "Breathe in for me Colonel."

"Well after I leave Elizabeth off at her quarters I go to Rodney's lab." John had another coughing fit. It was a deep, wet cough and boy was his chest starting to really hurt now.

"Rodney?" Carson listened to John's lungs some more as he instructed John to breathe in and out as deeply as he could for him.

"Yeah. He doesn't know when to quit either. Only he hasn't figured it out yet not like Elizabeth has. And he calls himself a 'genius'. Anyway, it takes a little longer with Rodney. Getting him mad enough to want to leave the lab or getting him to think it's his idea to quit keeps getting more difficult. I have to be careful. That's why I'm late getting back here." Carson was examining his throat inside and out.

"I don't like the way your lungs sound Colonel. Your skin is clammy too. You have slightly swollen glands and from the looks of it your throat is raw. And you do this every night?"

"Pretty much. Can't you just give me some cough syrup or something? I'm sure with a few hours sleep I'll be fine in the morning. Right now I just need to be warm. I've got to shower. I can't stand this mud anymore." John started to list to the right and would have fallen off the trunk had Carson not grabbed his bare shoulder.

"Colonel!" Beckett exclaimed reaching for the soldier.

"Sorry Doc. Just a little dizzy."

"When did you last eat?"

John thought about that for a minute. "Dinner. Had the meatloaf."

"Colonel there was no meat…loaf tonight. You haven't eaten anything since yesterday evening!"

John just shook his head no and headed for his bathroom grabbing the dry clothes the good doctor had handed him. Closing the door, but not all the way, as the Colonel knew the doctor would be listening right outside in case anything happened.

"My God Colonel what have ya been doing all day?" Exclaimed the doc through the partly closed door.

John ignored the doctor's remark he finished stripping and stepped into the shower. The warm water felt good against his clammy skin. It took an extra five minutes to fully get the mud that was caked in his hair to wash out. As he stepped out of the shower and dried off he turned his head towards the door where he knew Carson was standing and began his tale as he put on his sweatpants, shirt and socks. "Let's see …mudslide, debrief Dr. Weir and Col. Caldwell, off-loaded the Daedalus, helped Dr. Murray, brought supplies to the infirmary, searched armory, warehouse and east pier for two crates of missing weapons and ammunition, returned the children to the mainland, had less than an hour to write up an AAR for Col. Caldwell, sat in another debriefing, took Cpl. Mitchell's sentry duty, walked Elizabeth to her room and Rodney to his. I'm sure there were other things in there too, but that's the highlights. Now if you're not going to give me some cough syrup please go away," he stated as he came out of the bathroom and headed for his bed. "I've only had two hours of sleep in the last twenty-four hours. I'm tired."

John started coughing harder this time. And this time he coughed up a small amount of blood. His throat was so sore, raw it hurt to talk and he was getting cold, yet he was also warm at the same time. His headache was worse too. He grabbed his head trying to keep his brains from busting out after his last coughing attack. "Arraggghh."

"Into bed with ya now. I'll get Mary to bring an IV and we'll start you on some good antibiotics. I think you maybe gave yourself pneumonia Colonel. The blood on your hand is a good bet. And being in a wet uniform all day sure didn't help matters. Most people have the sense to come in out of the rain. Common sense to get out of wet clothes too. Most people even take the time to eat. I wish you would watch out for your own health as much as you watch out for everyone else's. Sometimes Colonel…"

"Hey I tried! I tried to tell you when you ordered me to take the children back. I tried but Elizabeth comm'd me three times about initial debriefing. You were there for two of those times. I tried in the jumper to tell her. Remember? I tried after the off-loading but Dr. Murray had broken her glasses and couldn't see where she was going. What did you want me to do? Leave her wondering the halls? I was there in your infirmary but two cases of weapons were missing which I personally signed off as being received. I tried to find someone to cover Cpl. Mitchell's duty but there just wasn't anyone left. More than a quarter of the Marines are down with this damn cold, another fourth are on mainland, a fourth resting up so they can go back to the mainland and the remaining Marines here in Atlantis are already pulling double shifts to cover. I can't help that Elizabeth and Rodney don't know when to call it quits. But what I do know is that they are important members of this expedition and I'll do whatever I have to. Even if it means I lose a little sleep over it so be it. Or end up staying in a wet uniform all day and not eating I'll do that too. You should know by now Doc that I will do what I have to, go to any length to protect Atlantis and all her people. I really tried Doc, I don't know how many times today I tried to get back here and out of those damn wet clothes but I did try, so don't go blaming all this on me…I…" John broke off his tirade and started coughing more blood speckled his hand.

"I'm sorry son. I just hate seeing ya like this." Carson tutted and got the Colonel under the covers while he looked around for his comm that he had taken off when he laid his head down on the desk. As soon as it was over his ear he knew the command channel had been activated. He pulled a couple of tissues from the box sitting on the desk and handed them to the Colonel. While the Colonel wiped the blood specs off his hands Carson reached down secretly to the nightstand to turn off the Colonel's radio. Activating his comm he called for an IV and stand, portable oxygen and a dose of antibiotics to be brought to the Colonel's room.

Carson wondered just how long the command channel had been activated as he replayed the events in his mind. He only hoped that it hadn't been long and pick up their _whole_ conversation.

John was dressed in a long sleeved t-shirt, sweatpants and socks that Carson had given him while he did his cursory exam and was shivering under the light bed covers. Carson went to the pilot's closet and found two more blankets to cover him up with. Mary chimed at the door a few moments later and the two started the IV and put the nasal cannula in place. The Colonel was too tired to argue about anything. Beckett took the dose of antibiotics and injected into one of the IV ports. Taking the Colonel's temperature again Carson found it to be 102.3. The shivering pilot closed his eyes and let exhaustion take its toll.

oOo

Dr. Weir was still sitting up in bed reading a romance novel she borrowed from Lt. Cadman when her comm activated on the command channel. _'What now'_ crossed her mind as she listened to the conversation on the other end. At first she could clearly make out Carson's and John's voices. Then a few minutes later barely made out what was being said. The voices seemed further away and muffled, like someone talking from behind a closed door or something. After several minutes John's voice came through loud and clear. From the sound of things he was unaware that he was broadcasting on the command channel. Clearly Carson and John were arguing. She kept listening and when she heard Carson say something about coughing up blood she jumped out of bed, slipped on some shoes and headed for the Colonel's quarters in her sweatshirt and pants continuing to listen to the military leader rant.

Rodney was just getting out of the shower when he heard his comm beep. Wrapping a towel around his waist he rushed to put the comm back on to see what other emergency was taking place in the span of twenty-four hours. You would have thought that a mudslide would be enough for one day. Although he hadn't had much to do with it he knew it had been a long day for most everyone. As he listened he heard muffled voices then Carson was complaining about being wet and someone not eating. Walking Beth and Ronny to their quarters. Blood. Then it really got heated when the Colonel started yelling back.

Rodney seemed to have lost his ability to multitask; he couldn't seem to listen and put clothes on at the same time. He had refocused his attention solely to listen to what the Colonel was yelling at Beckett about while getting dressed. Rodney couldn't believe what he was hearing. And who was Beth and Ronny? And why was the Colonel walking them to their quarters? The Colonel had been up since three am and after dealing with a mudslide he had to deal with issues back here on Atlantis. The Colonel always appeared laid back and lazy. He didn't look all that great now that he thought about it when the Colonel came to his lab earlier. Rodney heard some terrible coughing before the command channel was turned off. He finished getting his clothes on and ran out the door to the Colonel's quarters.

Meeting Elizabeth outside the door, neither one wanted to knock. "You heard?" Asked Rodney.

"Yes."

Before anymore could be said between them Mary and Dr. Beckett stepped out into the hallway. Elizabeth tried to peak over Carson's shoulder to see John but the lamp on the desk didn't provide enough light to see and the door shut too swiftly. Carson sent Mary on her way while he stood in the hall to talk to Elizabeth and Rodney.

"I'm sorry you had to hear all that. I wasn't aware the command channel had been activated." Carson apologized for the Colonel. "I had taken my comm off while I waited for the Colonel. Had I known…" Carson stated tiredly.

"Does John have pneumonia?" Elizabeth asked.

"I don't know lass. It could be just a bad cold and the blood he coughed up could be from his sore throat. It looked pretty raw. I'll know more in the morning. I have him on an IV and oxygen for tonight. I also gave him a strong dose of antibiotics. Right now it's important that he get some rest. The lad has only had two hours of sleep. And with all the exertion he's done today he's bone tired. Seems he didn't get to bed until after one am." Carson pointedly looked at Rodney when he said those final words.

"Why are you looking at me when you say that? Oh…hey he's the one…I don't need….I never asked…" The light just flicked on over Rodney's head as he realized it was 'he' who John was talking about. Rodney tried to blame the Colonel but knew it was wrong. He knew he got caught up in scientific discovery and he knew he spent way too many hours working in his lab. He just thought the Colonel couldn't sleep or enjoyed coming to his lab although he made a pest of himself most of the time until Rodney just couldn't stand it any longer and called it quits.

Just as Carson was going to continue talking three more people were running down the hall to join them. Even on the mainland the command channel must have broadcasted loud and clear.

"How is Colonel Sheppard?" Teyla asked a little out of breath.

"You heard?" Elizabeth looked between Teyla, Ronon and Major Lorne.

"Yes ma'am. We got here as soon as we could." The Major responded. "The first part didn't come through all that well, but that last part sure did."

"He's exhausted. Has a sore throat and I don't like the sound of his lungs. As I was about to tell Elizabeth and Rodney here, I will stay with him tonight and see how it goes. Hopefully rest and the antibiotics I've given him will be enough to knock it out of his system. Now you all should get some sleep. You three should get some dry clothes and food first. You've all had a long day and we'll talk more in the morning." Carson advised.

Ronon backed himself up against the wall and slid down. This wasn't the infirmary where he at least had an uncomfortable chair and could rest his feet on the bed rails, but it would do. He had sat on worse in his years of being a Runner. Teyla followed suit and dropped down next to Ronon on the hall floor. Rodney turned and ran down the hall. Everyone thought that he was upset at hearing the Colonel's admission. But instead Rodney was back a few minutes later with a tray laden full of snacks and copped a squat next to his other two team mates.

"Hey if you can't beat'em, join'em I say." As Major Lorne slid down the wall as well.

Carson huffed, "why do I even bother?" He mumbled as he shock his head in disbelief and went back into the Colonel's room to keep vigil.

Elizabeth didn't know what to do with herself. "Is that one of those pear things?" She asked pointing to the medium sized purple colored fruit on the tray Rodney brought back from the mess hall.

"Yes…yes I think it is. Join us?" Rodney picked up the purple colored fruit and offered it up to Elizabeth. She took it and found herself sliding down the wall to join the rest of them in staring at the Colonel's door. Rodney and Elizabeth filled in the three late comers as to what Dr. Beckett had told them before they arrived and what they heard over the command channel. Now it was just a waiting game to see how the Colonel was.


	2. Possible Ending Number 1

Possible Ending Number One

A/N: This story was not Betaed, all mistakes are my own.

Possible Ending Number 1 of: When It Rains It Pours

John woke relishing the feeling of warmth that surrounded and bathed him. He remembered being so cold, now he was warm and could easily go back to sleep. But his stomach had other ideas. John realized it had been close to thirty-six hours since he had eaten and his stomach was complaining tenfold. John managed to get his eyes open and found the doctor slumped back over his desk snoring just like he was when he came to his room late last night. His clock read 05:17. He carefully removed the IV needle from the back of his hand and pulled off the nasal cannula that had helped him breathe as he dug himself out from within the cocoon of blankets. John slipped out of bed quietly and managed to make it to his closet without waking the snoring doctor. John slipped his socked feet into his sneakers and moved towards the door.

The door opened with a silent swish and closed just as quietly after him. John was startled to see five figures lined up against the opposite wall all sound asleep. Including Ronon who he knew from missions didn't sleep that soundly. He took a moment to wonder why they were camped outside his door. The last he remembered Teyla, Ronon and Lorne were on the mainland. And he definitely remembered walking Elizabeth and Rodney to their own rooms last night. As his stomach growled once again, he smiled at them and headed for the mess hall for some much needed breakfast. There would be time later for questions and answers.

"Morning Sir. You're up early. What can I get for you?" Asked Airman Stockard who was on KP rotation this week as he was just setting up the chow line. "We have the usual, eggs, bacon, toast, muffins and oatmeal or if you're not in a hurry we will be serving pancakes."

It didn't take John all that long to decide. "I'll take two pancakes Airman." John said with a hungry smile.

"Coming right up Sir. It'll just take me a couple of minutes. I'll bring them to you."

The Colonel nodded and filled a glass with milk, grabbed some utensils, butter and syrup and sat down. The mess hall was relatively quiet at this hour with the exception of the occasional pot or pan banging coming from the kitchen. He watched as the mess staff made several trips back and forth setting up the morning buffet line. Soon the mess hall would be filled with hungry expedition members. In no time at all the Airman delivered two steaming hot golden-brown pancakes to his table. "Thanks Airman. Would you do me another favor if you have time? I need five cups of coffee, one Athosian tea and one large glass of milk to go. Say in twenty minutes."

"Sure thing Sir."

John turned back to his breakfast he spread butter and poured syrup before he dug into his pancakes enjoying every bite and washing it all down with his glass of milk. At first he wasn't too sure how his sore throat would handle the sweet cakes but after his second bite it was not an issue. They went down nicely and for that his stomach was grateful. When he finished he returned his empty dishes and picked up the tray that Airman Stockard had just prepared for him.

Carefully he navigated down the empty hallway trying not to spill the contents of his tray. When he reached his still sleeping friends he thought how stiff their necks will be when they woke up. John couldn't image that sleeping like that would be comfortable and the question still remained was _why_? Ronon's and Teyla's room was just around the corner from his. Rodney was on the next floor up, Elizabeth was in section six and Major Lorne's room was one hallway away from where most of the military bunked. Yesterday had been a long day that blurred in time as John racked his brain why his friends would be camped outside his room but kept drawing a blank. John lightly tapped Ronon's foot. Once his eyes were open, John handed him the large glass of milk from his heavy tray. He nodded to Ronon to nudge Teyla and handed her the Athosian tea. When she moved to take the hot cup it woke Rodney up as he had his head resting on her shoulder. _At least he wasn't drooling this time._ John laughed inwardly at the thought. John handed Rodney a cup of coffee indicating he should remain quiet. Rodney took the cup and after a couple sips began working out the kinks in his neck as silently as he could.

John tapped Evan on the boot. He had his arms folded crossed and his chin rested on his chest. As Evan woke enough John handed him his wake up cup of coffee. By the time he got to Elizabeth she had already roused. Her eyes were open and accepted the hot cup with enthusiasm and a warm smile. Before he could start asking why they were all sitting outside his door, Beckett burst out of his room in a panic shouting into the hallway "he's gone!"

"Who's gone?" John asked concernedly holding the tray with the last two cups of coffee on it.

Carson finally took a moment to get his bearings and noticed that Elizabeth and the rest, still sitting on the floor, all had wide smiles on their faces.

"Here Doc I think you might need this." John offered him a cup of coffee to help him wake up.

Carson took the offered cup and swallowed down a few sips. "Where did you get off too Colonel?"

"The mess hall. I was starving when I woke up. They're serving pancakes this morning. You were snoring at my desk and these guys were asleep out here. Which reminds me why…?" He started to ask.

"Did you say pancakes?" Ronon interrupted as he got himself to his feet.

"Yeah. Hot of the grill too." John added.

Slowly the rest of his friends pulled themselves off the floor and into a standing position. He offered Elizabeth a hand up, while Rodney helped Teyla to stand. John was just reaching for his coffee when Beckett stopped him cold.

"I don't think so Colonel. The last thing you need is caffeine." The doctor took the cup away from him in a move that would make Bruce Lee proud.

"I'll take it!" Rodney moved over to Carson and took it greedily. Rodney had already inhaled the first cup.

"Hey!"

"Sorry Colonel, no coffee for you. That's the last thing you need right now. What you do need is sleep. You're heading back to bed this very instance. Fours hours is not enough after the day you had."

"Carson I'm fine. Whatever you gave me last night…it worked. I feel great and besides I have several reports to get done, I need to make out a new schedule for the Marines. There's still the Athosian settlement and I…"

"No Colonel. No reports, no settlement, no work of any kind. You're heading back to bed. You _will_ let me examine you and you _will_ do as I say." Carson stated in a no nonsense tone.

"Guys…help me out here." John pleaded to his friends. "I'm fine."

"You're on your own Sheppard. I'm with Conan here and pancakes sound really good this morning." Shouted McKay as he and the rest of his friends started to trail down the hall towards the mess hall.

"Sorry Sir. The Doc outranks us both." Offered Lorne with a quirky sympathetic grin as he too followed McKay and Ronon to the mess hall.

Feeling deserted he turned to Teyla and Elizabeth. "Teyla? Elizabeth? Help me out here. I'm fine…really."

"Sorry John, you heard the doctor. Get some rest. We'll talk later." She gave him a pat on the arm and took the empty tray he was still holding. She walked away barely containing her amusement of the situation.

"But…"

"Rest well John." Teyla offered with a pat on his shoulder.

"But…I'm fine!" He yelled after them as Carson grabbed an elbow and steered him back into his quarters. "I'm fine."


	3. Possible Ending Number 2

Possible Ending Number Two

A/N: Medical jargon is not my forte, so please be understanding. This story was not Betaed, all mistakes are my own.

Possible Ending Number 2 of: When It Rains It Pours

A clanging noise an hour or so later brought the five wall huggers up to their feet. Running down the hall pushing an empty gurney were two nurses. The nurses and the gurney entered the Colonel's room without any pause or acknowledgment of their presence. The door swishing shut behind them. The five looked on in awe not knowing what was happening inside.

The door opened again, "Major, Ronon could you give us a hand in getting the Colonel on the gurney please." Carson said swiftly.

Ronon and Major Lorne entered the room to help the doctor. Elizabeth, Teyla and Rodney stood in the doorway and watched as the three men and two nurses lifted the Colonel onto the waiting gurney. The three were almost run over by the fast moving gurney. Carson was barking out orders as they swiftly moved down the hall towards the infirmary. Closely followed by five worried souls.

Entering the infirmary Carson continued his list of orders. "I want a chest x-ray, CBC and arterial blood gases. I also was a culture of the Colonel's sputum. Alright now, gently…let's get him comfortable. Mary would ya raise the head of the bed up? That should help alleviate some of the stress on his lungs. Doris, get the warming blanket please luv. Okay let's get that blood sample and tell the lab to rush it."

Mary got the blood sample and rushed it off to the lab. Doris put the warming blanket on and replaced the nasal cannula with an oxygen mask. Taking a new set of vitals and reporting them out loud to Dr. Beckett.

The Colonel became aware enough that he knew he was no longer in his bed or his room for that matter. The distinct smell of disinfectants was a major clue-in as were the subtle beeps off to his left. But there was something else that was bothering him. He was aware of the IV and the presence of the catheter, but still something else. He finally managed to open his eyes to take in his surroundings. There, he spotted it hanging from the IV stand he had an NG tube feeding him God only knew what.

His hand came up to his face to take the mask away but another hand stopped it before he could reach it. "You leave that alone. You need both the oxygen and the nutrients." Carson quietly informed his patient.

"Hrrtts…" John tried to say. The oxygen mask was pushing against the NG tube and it was uncomfortable to say the least.

"You have pneumonia Colonel. You're going to be my guest for a while now go back to sleep, rest is what you need right now."

John let his eyes close and went back to sleep as he was told.

Three days later John woke again. He opened his eyes but everything in his field of vision was blurry no matter how much he blinked or rubbed his eyes. The oxygen mask was gone but he still had the NG tube, IV and catheter. He just couldn't understand why his vision was so wonky.

Carson came to check on his number one patient and found his eyes open but worried. "Are you with us Colonel? You've been in and out, well mostly out for three days now."

John turned his head toward the Scottish brogue. "I think so. But I can't seem to focus everything is blurry Doc." He admitted. For a pilot you need 20/20 vision and right now blurry was scary.

"Your eyes are fine Colonel. I have you in an oxygen tent. You were struggling with us to remove the oxygen mask. I thought using an oxygen tent would be better than putting you in restraints. If you keep improving we should be able to remove the tent in four or five days. Your lungs are sounding better everyday. Does your chest still hurt when you breathe in?"

John took a tentative breath inward and found that his chest did not feel like an elephant was sitting on it much like it had before. "No it seems fine. How long have I been here?"

"Five days so far, working on six. Do you feel up to some company? Your team has been under foot. I finally chased them out last night so if you think you could stay awake long enough I could contact them for you." Carson offered knowing how close the Colonel was to his team and vice versa.

"If it's okay with you, maybe later." John replied through a yawn.

"Alright lad, later. Get some rest it's the best thing for ya right now."

And so the Colonel did…rest.

"…is he going to wake up? I thought you said he was more lucid today." Rodney harped to no one in particular. He, Teyla, Ronon and Elizabeth all stood looking between the sleeping man and the tired doctor.

"Hush Rodney. The Colonel will wake up when he is ready." Carson chided.

A mumbled sound came from the head of the bed. "'m wake."

Elizabeth and Teyla took positions on either side of his bed closest to him. Snaking their hands under the clear plastic of the oxygen tent to hold or in Elizabeth's case squeeze his hand. Ronon stood at the foot of the bed while Rodney crowded up behind Elizabeth and Carson stood behind Teyla.

It took him a while after he mumbled he was awake for his hazel eyes to finally open. Doing his best to focus on the figures around his infirmary bed. He saw Teyla first and thoughts of the mudslide came back to him, his concern for her and her people foremost on his mind. "Are the Athosians okay?" He rasped his throat still sore and he fought against his gag reflex of the tube running down it.

"Yes John. My people are doing well. You and your men have been of considerable support to us. It should not be long before our settlement will be whole again. My people wish you well and give many thanks. Once you are well and rested they have requested that you return for the celebration of New Beginnings."

"I didn't do much Teyla. You should get the Marines and the Doctors to come to your celebration." John didn't deserve the attention he hadn't done much at all. He'd been out of if for almost a week now while life around him went on. He didn't even know if it had stopped raining.

"They are also invited. But we will wait until you can attend also." Teyla said matter-of-factly.

"John you look tired maybe we should leave and let you get some rest." Elizabeth had noticed that he was beginning to slur his words and his eyes kept closing.

"'kay."

Day seven of his infirmary stay John woke to a warm feeling on his face and a warm hand clasped around his. His face automatically smiled at the warmth and comfort that surrounded him. When he opened his eyes the sun was shining down on him from the infirmary window. It was a beautiful sight to wake up too.

He was still in his clear tent. He managed to focus on Elizabeth who was clasping his hand. "Hey."

"Hey yourself." Returning his smile with one of her own. "How do you feel?"

"Better. Tired."

"Pneumonia will do that I've heard."

"I'm finding that out." He said with a smile as his eyes slid closed and he slept.

The next time he woke the oxygen tent was gone and he heard the familiar clicking of someone typing. As he turned his head to the left he found Rodney; sitting in the chair that Elizabeth last occupied, with his laptop on his knees working away.

"How long?" John rasped. Hoping that McKay would know what he meant.

Rodney stopped typing and looked up. "Eleven days so far."

"Rain?"

"Stopped about a week ago." Rodney paused a moment before getting up enough nerve to continue. "I'm sorry, you know. I just get wrapped up in my work sometimes. Well…anyway, I'm sorry."

"You're a challenge McKay. I like challenges. We're good…right?"

Smiling he answered. "We're good Colonel."


	4. Possible Ending Number 3

Possible Ending Number Three

A/N: Techno-babble is not one of my forte's, so please be understanding. This story was not Betaed, all mistakes are my own.

Possible Ending Number 3 of: When It Rains It Pours

On his third such day of mandatory rest he was surprised to see Elizabeth coming through his door with his lunch. Carson had refused to allow his team mates to visit. Dr. Beckett knew they wouldn't be able to keep their mouths shut about the daily goings on and he wanted the Colonel to rest.

"You're a sight for sore eyes." He stated the old saying.

"Well…" She started saying putting the tray of food down on his desk. "It took me all morning to convince Carson to let me see you. He says you're doing fine by the way."

"Yeah I know. He told me the same thing this morning but he still won't let me out. Or even let me have my laptop or comm back. I don't know what's going on out there. He won't let Rodney, Teyla, Ronon or Lorne visit. I don't suppose you could smuggle my laptop or even a comm link in for me. I'm going crazy in here. I actually read more of 'War and Peach' that's how desperate I am. If I only had my laptop..."

"Carson wanted you to rest. You were exhausted, run down and nearly on the brink of getting pneumonia." Elizabeth stated factually.

John sat down at his desk and played with his food as he thought about it. Elizabeth was right, so was Carson. He just hated to not be in 'the loop'.

Elizabeth had settled on the end of his bed quietly watching. "Can I ask you a question?" Elizabeth asked breaking the silence of the room.

"Sure."

"How much do you remember from the day of the mudslide?" She asked.

"All of it, why?"

"Do you remember yelling at Dr. Beckett?"

"Yeah…I apologized to him when I woke up later that same day I think. I really hadn't been lucid much before that. Why did he say something to you?"

"No. It's just…" Elizabeth paused to get her thoughts in order. "…just you ended up broadcasting your little tirade on the command channel."

"Oh God…please tell me not everyone heard it." John dropped his fork on his tray and stared at Elizabeth he could tell by the look on her face that indeed all command staff heard his little outburst with the good doctor. John sank back into his office chair. "Is McKay upset at me?" He whispered.

"No he's not upset. How long have you…"

"About the same time as you. Only you figured it out way early."

"John that's been four years now." John nodded in affirmation. "What about all that other stuff that happened. Are your days on base filled with escorting blind doctors to their quarters? Inventorying armories and God only knows what else." Elizabeth wanted to know.

"Other than the mudslide that day was mild compared to most." John deadpanned with his most serious look.

oOo

John was making his nightly rounds. Carson had finally allowed him back on duty this morning. He had spent most of the day catching up on reports about the mudslide as well has writing a more detailed AAR for Col. Caldwell on said incident. A majority of the Marines had reported back to duty and they were almost at full compliment status. As he walked the halls checking on his Marine patrols and staff in general he worked his way to the command center. He came to an abrupt stop when he saw Elizabeth's office was dark. He turned and asked the technician on duty where Dr. Weir was.

"Dr. Weir left about forty minutes ago Sir." The technician reported.

"Did she say where she was going?"

"She just said she was 'calling it a night' Sir."

"Thanks." With that John turned around and headed for Rodney's lab. He'd just be earlier than usual and maybe get the chance to apologize to Rodney for anything he might have heard during his recent rant on the command channel.

Walking down the hall towards McKay's lab John noticed that the lights were dim. He wondered if there was a power problem he hadn't been made aware of but as he got closer he found the lab dark and empty. Checking his watch it was only 22:37. Rodney _never_ stopped this early.

Over the next couple of days each evening when he made his rounds he found Dr. Weir and Dr. McKay had seemingly turned in early.

So tonight he tried a different tactic. Instead of Dr. Weir's office, he went to her quarters. As he stood waiting to be let in after activating the chime he wondered if she could actually be in bed and that he would be disturbing her. But as the door slid open he got his answer. She was still dressed in her uniform and the laptop was open. It was obvious that she was working.

"May I come in?" John asked.

"Yes of course. Please." Elizabeth looked like she had been caught red handed in the cookie jar. "Here…sit down." She motioned toward the lounge like chair she had in her room while she resumed her spot in her desk chair.

"Elizabeth you don't have to do this. I'm sorry I made you feel self conscious." John blurted out. "That was not my intent."

"Do what?"

"Hide in your quarters. That's what you've been doing these past few days haven't you?" John stated what he knew to be fact.

"No." But John could see that she was lying.

"Rodney's doing the same isn't he? I've gone to his lab every night and it's always the same. I'm really sorry. I had no idea that I was broadcasting my little rant. Carson had said some things…well he made me a little upset and I was…Look I didn't mean for you and Rodney to feel bad. I like walking you to your quarters each night the same as I like trying to get Rodney to quit working on whatever he's doing for the night. It's a challenge. So can we please go back to the way things were before my little outburst?" John finally asked.

Elizabeth had the decency to look a little embarrassed at being caught. It had taken John less than a week to figure it out. When it had taken her several months to realize what he was doing all these many years ago. The smile on her face told John everything he needed to know.

"So…where's McKay hiding?" John inquired.

"Level 3, Lab Six."

"Thanks…and goodnight."

John could hear Rodney talking to himself halfway down the hall as he approached Lab Six. "Whatcha working on McKay?" John asked stepping into the lab.

"Oh…just trying to get…" Rodney looked up in surprise as he realized Sheppard was the one who asked.

"Trying to get 'what' Rodney?" John asked for clarification moving further into the room.

"Trying to get the ratio of the sensor frequencies to sync up with the algorithms needed for distance transference so we can get better use out of our long range and short range sensor sweeps."

By the time Rodney finished telling the Colonel what he was working on, Sheppard was looking over his shoulder at the lines of data scrolling across the screen.

"Here…" John pointed to a section on the screen. "…you need to change that equation to consider the x and y variables. Then it should sync up."

Rodney studied the section that the Colonel just pointed out and realized he was correct. He began typing in the corrections and within minutes he had his sensor frequencies in sync with the sensor sweeps.

"Thanks."

"You're welcome. Anything else I can help you with before we turn in for the night?"

"No…no that was all I was working on. Now that it's running properly I can call it a night." McKay exclaimed.

John walked Rodney to his quarters and said "goodnight".

"Night Colonel." Rodney replied back in kind. He was taking a step into his room when he realized what just happened. "Hey…you did it to me again!" He shouted down the hall at the retreating Colonel.

"I have no idea what you're talking about McKay. Goodnight." John smiled and continued walking down the corridor without turning around.


End file.
